A five-year inquiry into the government's academies programme has concluded that there is no "academy effect" and while results in the schools have improved overall, GCSE marks reveal a mixed picture.

The 130 academy schools are benefiting from expert sponsors, state of the art buildings, and being able to pay teachers above the odds. But there are now questions about whether they are beginning to select high-achieving pupils and whether the high premium ministers place on the scheme is detracting from other schools.

"Rather than a simple uniform 'academy effect', there has been a more complex and varied process of change," the report, by consultants at PriceWaterhouseCoopers and commissioned by ministers, concludes.

It says that some academies have used vocational courses to "secure higher and faster improvements" in results and when the schools are measured on GCSEs including English and maths the process is "less substantial".

There has been an "important policy shift" with academies losing some of their independence, and being made to teach the national curriculum and work much more closely with local authorities, the report shows.

It reveals how the academy programme of independently managed but publicly funded schools has changed radically since its inception.

Initially sponsors were mostly white, male businessmen and now sponsors are more likely to be groups of universities, local authorities and educational trusts and charities.

The schools are increasingly teaching the national curriculum and abiding by teacher pay conditions. Though some started off introducing radical teaching techniques, they have gone "back to basics" focusing on rigorous teaching and testing pupils to identify those lagging behind.

The shifting nature of the programme means it is impossible to identify an "academy effect", the report says. Many schools are adopting the techniques and management processes which are common to all improving schools, whether academies or not.

It clears academies of a key allegation made against them: they have not disadvantaged local community schools. The researchers compared the 24 first academies with the national average and other schools in similar circumstances. There is no evidence that as they have improved in status they have caused neighbouring schools to sink, they found.

Academies are employing more teachers without qualified teaching status – 12% are not qualified compared with 5% in the state sector, the report said. By doing so, some are breaking their funding agreements which require all teachers to be qualified.

The report raises new concerns about the accountability of the funding of academies. It says that the accounts provided by academy sponsors for the running of their school don't always match up to the accounts of the department for children, schools and families. "This missing link creates a potential risk in respect of the department's parliamentary accountability," it says.

The proportion of pupils from the poorest homes has dropped significantly in academies, the report says. It also highlights the high rate of exclusions in academies.

Benefits of academies were noted – including sponsorship, ability to recruit top teachers and their state of the art buildings. But the reports says there are also challenges with the schools, including: "ensuring fair and equitable access for all pupils, and particularly those from disadvantaged backgrounds for whom the programme was originally intended".

Jim Knight, the schools minister responsible for academies, said: "This PwC report shows academies are improving results at a faster rate than the national average and that sponsors bring added value thanks to strong leadership and drive. The report says that governance in academies is generally good and the quality of leadership is generally very good.

"This is significant as PwC have done an independent study on school leadership that shows good leadership and management leads to good teaching and learning in the classroom. The report also points out that academies are popular with parents – there are three applications for every academy place."